Integrate real-world street networks into VRP problems using OpenStreetMap data. Use when loading real map data, creating instances from actual locations, computing network-based distances, or building tutorials with real-world scenarios. Guides through installation, loading areas, extracting nodes, computing distance matrices, and creating PDPTW instances from map data.
Visualization patterns for sparse single-cell gene expression data. Trigger: boxplots flat at zero, single-cell expression plots, sparse data visualization
ArchR docs served from downloaded_docs/archr_scrape - comprehensive scATAC-seq analysis toolkit with all HTML files explicitly listed
Network meta-analysis for comparing multiple treatments
Phase 1 of MIP pipeline - Research Gatsby metaphor scholarship, establish seed CMT systems, and document MIP procedure for annotators.
Teach Trial Sequential Analysis (TSA) for controlling type I and II errors in cumulative meta-analyses. Use when users need to assess if meta-analysis has sufficient information, want to avoid premature conclusions, or need to plan future trials.
Isolates skin regions from background clutter using calibrated thresholds for downstream analysis
Fast repository indexing for RLM workflows. Use before analysis to reduce context drift.
Process bulk RNA-seq datasets for VEuPathDB resources
Machine learning integration patterns for rRNA-Phylo covering three use cases - rRNA sequence classification (supervised learning with sklearn/PyTorch), multi-tree consensus (ensemble methods), and generative tree synthesis (GNNs/transformers). Includes feature engineering, model training, hyperparameter tuning, model serving, versioning, and evaluation metrics for bioinformatics ML workflows.
R-based single cell analysis using Seurat v5 for .rds/.rdata files
Survival analysis methods including weighted logrank, MaxCombo, RMST, and milestone tests. Use when analyzing TTE data or choosing analysis methods for non-proportional hazards.
Complete meta-analysis generation for neurosurgical outcomes
SPATA2 空间转录组学分析工具包 - 100%覆盖414个核心文件（388个API参考+25个教程+1个主页）
Phase 3 of MIP pipeline - Cluster all metaphor annotations into 4 major CMT systems, with quantitative analysis.
evidence-scoutの結果を受け、研究ギャップを体系的にマッピングし、 新規性の高い研究機会を特定・スコアリングする。EHR-RWDの優位性を活かした差別化ポイントを明確化。
Group sequential design methods for interim analyses, alpha spending, and futility stopping. Use when designing trials with interim looks or implementing spending functions.
Optimizing segmentation feature extraction, SOM clustering, and spatial analysis for multiplex immunofluorescence imaging with cell compartment and ECM features
Best practices for writing efficient, clean Stan programs
Convert verbose memories to SSL v0.2 format - I am encoder AND decoder
Deep methodology knowledge for network meta-analysis including transitivity, consistency assessment, treatment rankings, and model selection. Use when conducting or reviewing NMA.
Face alignment, landmark extraction, and quality gating. Use when debugging alignment issues, reviewing rejected faces, or tuning quality thresholds.
